What should the Indians do with Chris Perez? Simple. Rehab his shoulder and pitch him. That's it. Don't do anything until Major League Baseball, or the legal system, says you have to. There is no reason to and they do not have grounds to do anything else.
Perez, like all Americans, is innocent until proven (or pleads) guilty. Even if it appears that the situation is headed that way, the team cannot act until the process is over. Also, a player cannot be disciplined by MLB until the legal situation is resolved. Perez has been charged, there are mug shots and a police report that does not sound good. There is plenty of smoke to this fire, but the team can't act until the fire is put out.